Genomics Core Facility

The Genomics Core Facility enables Saint Louis University investigators to use whole
genome methods in their research. Our services use high-throughput nextgen DNA sequencing
with the Ion Torrent Proton™ platform from Life Technologies.

Services include genome-wide RNA expression analysis (RNA-seq), genomic chromatin
immunoprecipitation using nextgen sequencing (ChIP-seq), and whole mammalian exome
and small genome sequencing. We can also apply the technologies to specialized applications,
such as mutation identification and targeted sequencing. Assistance with data analysis
is also provided.

Available Services

Genome-Wide RNA Transcript Analysis

Many biological questions can be addressed by determining the genome-wide patterns
of gene expression by measuring RNA levels. SLU’s Genomics Core Facility can provide
services including RNA isolation and data analysis, for Ion Torrent™ Proton nextgen
sequencing approaches to quantify mRNAs, non-coding RNAs and small RNAs such as microRNAs.
Depending on the method used, we can start with as little as 50 ng of total RNA.

Genome-Wide Chromatin Immunoprecipitation

Chromatin immunoprecipitation is used to determine where specific proteins bind chromosomes
and the locations of histone modifications and other epigenetic marks. This data can
provide insights into gene regulatory pathways and epigenetic control of gene expression.

The facility does not prepare chromatin or perform the immunoprecipitation but can
provide suggested protocols and advice for these experiments. Starting from input
and precipitated chromatin, the facility can use Ion Torrent™ sequencing to quantify
binding or chromatin mark enrichment genome-wide.

Exome and Small Genome Sequencing

Genetic variations in coding sequences of mammalian and smaller genomes can be discovered
by sequencing all known exons and comparing to reference sequences. The Ion Torrent™
also has the capacity to sequence entire small genomes for comparison to a reference
genome. We can generate sequences of small genomes for organisms that have not previously
been sequenced, but we currently do not provide genome assembly services.

Amplicon Sequencing

The Ion Torrent Proton™ sequencing technology is well-suited to sequencing specific
sets of genes or other features, such as all known oncogenes, starting with as little
as 10 ng of genomic DNA. This feature is useful for re-sequencing of particular gene
sets of interest. Life Technologies has many pre-designed amplicon libraries, and
custom amplicon libraries can also be designed using web-based tools.

Custom Projects

In addition to standard nextgen sequencing services (RNA-seq, ChIP-seq, exome, genome
and amplicon sequencing), custom sequencing protocols can be designed, such as sequencing
of selected oligonucleotide libraries. We can also design protocols for measuring
nascent RNA and run-on transcription approaches.

Nucleic Acid Quality Analysis

The core facility uses a Qubit™ fluorometer to quantify small amounts of RNA and DNA.
Detailed analysis of size distribution, quantity and quality is performed using an
Agilent bioanalyzer. Quality analysis can be provided as a service independent from
nextgen sequencing for a nominal cost.

Data Analysis

The core facility has installed Partek™ software to facilitate analysis of nextgen
sequence data, including gene ontology and pathway analysis. Partek™ provides a graphical
user interface that makes it easy for users to conduct their own analysis but the
core facility can also conduct the analysis for users. There is an hourly charge for
the use of the Partek™ software to cover the cost of the yearly license. Ion Reporter™
software uses cloud computing to detect genetic variations, such as SNPs, insertions,
deletions and CNVs in genome sequence data.

How to Start a Project

All projects are initiated by consultation with Dale Dorsett and Kathie Mihindukulasuriya
to design protocols that address the project in an efficient and cost-effective manner.
There is no charge for a consultation.

Project Pricing

The Genomics Core Facility aims to make genomic methods both affordable and timely
for SLU researchers. All charges are based on time and materials (microarrays, sequencing
chips and reagents).

Sequencing uses the Ion Torrent Proton, which can complete runs within two days and
does not require multiple simultaneous projects for cost-effective operation.

Contact Dale Dorsett to discuss your proposed project and obtain a detailed cost estimate
and a projected timeline for completion. The quote will include all materials, labor
costs, equipment usage fees and software licensing. Cost comparisons for different
approaches can also be provided.

As an example, a typical mammalian genome-wide RNA transcript quantification experiment
with three control and three experimental replicates (six total samples) will cost
between $3,000 and $3,500, depending on whether or not you isolate the RNA or do your
own bioinformatic analysis.